Among the nucleotide sequences of flaviviruses that include Zika virus, Dengue virus, yellow fever virus, Japanese encephalitis virus and West Nile virus, those of the Zika virus and Dengue type 2 virus are believed to share a high degree of similarity as can be commonly shown by BLAST pairwise analysis. Our study of the nucleotide sequences of the envelope and NS5 genes shows that the sequences of the Dengue type 2 virus are sharply different compared to other aforementioned human infecting flaviviruses. This is emphatically seen in a 2D graphical representation where each axis represents a nucleotide base and distinctly discriminated in terms of relevant RNA descriptors. The descriptors indicate the quantitative spread of nucleotide sequence graphs. In this report, we demonstrate this difference in terms of base distribution in the gene sequences through various parameters and consider possible reasons for such variations that seem to have been largely neglected in the literature.